Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

Skennerton, Connor T., Imelfort, Michael and Tyson, Gene W. (2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Research, 41 10: e105.1-e105.10. doi:10.1093/nar/gkt183

Author Skennerton, Connor T.
Imelfort, Michael
Tyson, Gene W.
Title Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2013-03-19
Year available 2013
Sub-type Article (original research)
DOI 10.1093/nar/gkt183
Open Access Status DOI
Volume 41
Issue 10
Start page e105.1
End page e105.10
Total pages 10
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Subject 1311 Genetics
Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history of phage infections and provides a direct link between phage and their hosts. All current tools for CRISPR identification have been developed to analyse completed genomes and are not well suited to the analysis of metagenomic data sets, where CRISPR loci are difficult to assemble owing to their repetitive structure and population heterogeneity. Here, we introduce a new algorithm, Crass, which is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set. CRISPR in assembled data are often fragmented across many contigs/scaffolds and do not fully represent the population heterogeneity of CRISPR loci. Crass identified substantially more CRISPR in metagenomes previously analysed using assembly-based approaches. Using Crass, we were able to detect CRISPR that contained spacers with sequence homology to phage in the system, which would not have been identified using other approaches. The increased sensitivity, specificity and speed of Crass will facilitate comprehensive analysis of CRISPRs in metagenomic data sets, increasing our understanding of phage-host interactions and co-evolution within microbial communities.
Keyword Biochemistry & Molecular Biology
Biochemistry & Molecular Biology
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DP1093175
Institutional Status UQ
Additional Notes Article number e105

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Chemistry and Molecular Biosciences
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Created: Tue, 26 Mar 2013, 19:11:57 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences